Mercurial > repos > bgruening > ctb_rdkit_descriptors

annotate rdkit_descriptors.py @ 8:2d051db1f561 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
author bgruening
date Wed, 17 Feb 2021 12:58:03 +0000
parents 81233a9053f5
children 87e62bbb4901
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1 #!/usr/bin/env python
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2
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3 import argparse
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4 import inspect
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5 import sys
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6
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7 from rdkit import Chem
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8 from rdkit.Chem import Descriptors
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11 def get_supplier(infile, format='smiles'):
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12 """
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13 Returns a generator over a SMILES or InChI file. Every element is of RDKit
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14 molecule and has its original string as _Name property.
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15 """
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16 with open(infile) as handle:
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17 for line in handle:
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18 line = line.strip()
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19 if format == 'smiles':
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20 mol = Chem.MolFromSmiles(line, sanitize=True)
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21 elif format == 'inchi':
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22 mol = Chem.inchi.MolFromInchi(line, sanitize=True, removeHs=True, logLevel=None, treatWarningAsError=False)
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23 if mol is None:
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24 yield False
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25 else:
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26 mol.SetProp('_Name', line.split('\t')[0])
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27 yield mol
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30 def get_rdkit_descriptor_functions():
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31 """
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32 Returns all descriptor functions under the Chem.Descriptors Module as tuple of (name, function)
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33 """
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34 ret = [(name, f) for name, f in inspect.getmembers(Descriptors) if inspect.isfunction(f) and not name.startswith('_')]
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35 # some which are not in the official Descriptors module we need to add manually
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36 ret.extend([('FormalCharge', Chem.GetFormalCharge), ('SSSR', Chem.GetSSSR)])
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37 ret.sort()
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38 return ret
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40
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41 def descriptors(mol, functions):
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42 """
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43 Calculates the descriptors of a given molecule.
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44 """
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45 for name, function in functions:
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46 yield (name, function(mol))
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48
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49 if __name__ == "__main__":
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50 parser = argparse.ArgumentParser()
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51 parser.add_argument('-i', '--infile', required=True, help='Path to the input file.')
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52 parser.add_argument("--iformat", help="Specify the input file format.")
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53
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54 parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'),
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55 default=sys.stdout,
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56 help="path to the result file, default is stdout")
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57
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58 parser.add_argument('-s', '--select', default=None,
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59 help="select a subset of comma-separated descriptors to use")
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61 parser.add_argument("--header", dest="header", action="store_true",
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62 default=False,
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63 help="Write header line.")
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65 args = parser.parse_args()
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66
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67 if args.iformat == 'sdf':
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68 supplier = Chem.SDMolSupplier(args.infile)
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69 elif args.iformat == 'smi':
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70 supplier = get_supplier(args.infile, format='smiles')
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71 elif args.iformat == 'inchi':
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72 supplier = get_supplier(args.infile, format='inchi')
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73 elif args.iformat == 'pdb':
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74 supplier = [Chem.MolFromPDBFile(args.infile)]
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75 elif args.iformat == 'mol2':
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76 supplier = [Chem.MolFromMol2File(args.infile)]
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78 functions = get_rdkit_descriptor_functions()
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79 if args.select and args.select != 'None':
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80 selected = args.select.split(',')
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81 functions = [(name, f) for name, f in functions if name in selected]
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83 if args.header:
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84 args.outfile.write('%s\n' % '\t'.join(['MoleculeID'] + [name for name, f in functions]))
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86 for mol in supplier:
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87 if not mol:
054d7b0de5c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
88 continue
8
2d051db1f561 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
bgruening
parents: 2
diff changeset
89 descs = descriptors(mol, functions)
2d051db1f561 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
bgruening
parents: 2
diff changeset
90 try:
2d051db1f561 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
bgruening
parents: 2
diff changeset
91 molecule_id = mol.GetProp("_Name")
2d051db1f561 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
bgruening
parents: 2
diff changeset
92 except KeyError:
2d051db1f561 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
bgruening
parents: 2
diff changeset
93 molecule_id = Chem.MolToSmiles(mol)
2d051db1f561 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
bgruening
parents: 2
diff changeset
94 args.outfile.write("%s\n" % '\t'.join([molecule_id] + [str(round(res, 6)) for name, res in descs]))